Best-selling author Michael Lewis’s new book, “Flash Boys,” has caused the debate over high-frequency trading to heat up once again.

During a Sunday interview on the news show “60 Minutes,” Mr. Lewis said the U.S. markets are “rigged” in favor of high-speed traders who use supercomputers to jump rapidly in and out of markets. The comments have triggered a sharp backlash on Wall Street, with some saying Mr. Lewis offers an incomplete look at the situation.

“He has not portrayed the full story of the U.S. equities market, leaving much on the cutting-room floor,” said market-structure expert Larry Tabb, CEO and founder of the research firm Tabb Group. “The market may not be perfect, but it’s not rigged,” he added.

Mr. Tabb has been following the rise of computer trading for years and has been on record praising the market’s efficiency, due in part to the liquidity provided by high-speed traders. But he has also said high-speed firms need to be more open about how they operate. And regulators need to move swiftly to catch up and give investors confidence that they aren’t being abused.

“While our markets are fragmented, there is significant benefit to having a fragmented market: competition,” he said. “While economic theory represents that the most efficient market is one where all orders interact and compete in a central limit order book, this theory falls down when it runs headlong into a market devoid of competition.”

High-speed traders have a diminished impact on the market now than they did five years ago, Mr. Tabb says. In 2014, HFT firms are expected to generate $1.3 billion in revenue, down from $7.2 billion in 2009. At the same time, trading costs for retail investors have declined in recent years and so-called “equity execution” has become less expensive, faster and more open, he says.

And high-speed traders provide benefits in the form of price discovery. “While virtually everyone hates speculators, the fact is that they do form what is one of the most important functions of a market – determining price,” he said. “Market makers, speculators, proprietary traders, HFT – no matter you call them – stand willing to buy and sell virtually 8,000 U.S. equities across the trading day, providing quotes to the market, which forms the basis of price discovery.”

The investigation, launched about a year ago, involves a range of trading activities and is still in its early stages, WSJ reported, citing a senior FBI official and an agency spokesman. Among the activities being probed is whether high-speed firms are trading ahead of other investors based on information that other market participants can’t see.

Mr. Tabb has said the Securities and Exchange Commission should not implement new regulations that restrict markets in favor of high-speed trading. Bottom line: “Brokers’ algos are not perfect. No trading machine, be it silicon or human, is perfect. The idea, however, is to create a more perfect and more efficient market. That is what competition and freedom are about,” Mr. Tabb said. “No, Mr. Lewis, the markets are not rigged.”

UPDATE: Mr. Tabb has said the Securities and Exchange Commission should not implement new regulations that restrict markets in favor of high-speed trading. An earlier version of this post incorrectly said the SEC should implement new regulations.